title: KO, scRNAseq

status: Public on Apr 24 2024

city: Austin

first: Qi

last: Tan

state: MN

address: 801 16th Ave NE

department: The Hormel Institute

institute: Univesity of Minnesota

description: 10X Genomics

data_processing:
scRNA-Seq data were aligned and quantified using the 10X Genomics Cell Ranger Software Suite (v6.1.1) against the mouse reference genome mm10 from raw count data
Assembly: mm10
Supplementary files format and content: Tab-seprated vallues files and matrix files

extract_protocol:
Cells were harvested and disassociated into single-cell suspensions following stardard FACS sorting method for mice lung tissue.
10XscRNA3Prime(10XscRNA3)

value: Lung

value: Cebpa KO


title: FF, scRNAseq

type: SRA

country: USA

description: 10X Genomics

library_source: transcriptomic single cell

molecule: total RNA

organism: Mus musculus

source_name: Lung

tag: tissue

tag: genotype

value: Cebpa FF


title: L_Mo

status: Public on Apr 16 2024

city: Shanghai

first: He

last: Fei

address: 801 Heqing Road

department: Department of Obstetrics and Gynecology

country: China

institute: Shanghai Fifth People’s Hospital

library_source: transcriptomic

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2 v2.0.5.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

molecule: polyA RNA

organism: Homo sapiens

source_name: HLECs

growth_protocol: hLEC treated for 24h with conditioned media of Cervical Cancer cells with 5% CO2 at 37℃

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols

treatment_protocol: Cervical cancer cells were cultured in DMEM supplemented with 10% of FBS until they reach 80% of confluence.Medium was then changed to ECM without FBS for 36 hours. This medium was collected, centrifuged for 5 minutesat 1500 rpm and filtered throught a 0.45mm pore membrane before use.The conditioned medium was prepared from the collected medium and the normal medium (ECM medium +5%FBS+1% ECGs+1% P/S double antibody) in a ratio of 6:4.

value: HLECs

tag: cell line

tag: cell type

value: Primary Human Lymphatic Endothilial cells (hLECs)

value: MDK overexpress

tag: treatment

value: hLEC cells was used at 60%-70 confluency.  The media was substituted by 36h conditioned media from MS751 MDK.  Cells were left to grow for 24h before being collected and processed for RNA-seq anlysis.


title: L_Mo2


title: L_Mnc

value: MDK NC

value: hLEC cells was used at 60%-70 confluency.  The media was substituted by 36h conditioned media from MS751 NC.  Cells were left to grow for 24h before being collected and processed for RNA-seq anlysis.


title: L_Mo1


title: Posterior segment, Runt RNAi, 0 day post-injury, replicate 3

status: Public on Apr 09 2024

city: Stanford

first: Yuan

last: Xue

state: CA

address: 318 Campus Drive

institute: Stanford University

description:
RNA-seq
dpa_bulk_NPv6.tar
231202_231220_dpa_Illumina_SmartSeq2_bulk_NPv6/tables/NPv6_Illumina.algae.TPM.tsv.gz
231202_231220_dpa_Illumina_SmartSeq2_bulk_NPv6/tables/NPv6_Illumina.counts.tsv.gz
231202_231220_dpa_Illumina_SmartSeq2_bulk_NPv6/tables/NPv6_Illumina.algae.counts.tsv.gz
231202_231220_dpa_Illumina_SmartSeq2_bulk_NPv6/tables/NPv6_Illumina.sample_annotation.tsv.gz
231202_231220_dpa_Illumina_SmartSeq2_bulk_NPv6/tables/NPv6_Illumina.acoel.counts.tsv.gz
231202_231220_dpa_Illumina_SmartSeq2_bulk_NPv6/tables/NPv6_Illumina.TPM.tsv.gz
231202_231220_dpa_Illumina_SmartSeq2_bulk_NPv6/tables/NPv6_Illumina.acoel.TPM.tsv.gz

data_processing:
We filtered Illumina reads using Trimmomatic (v 0.39) with the following parameters “LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36”, and Nanopore and Pacbio reads using NanoFilt (v 2.7.1) with the following parameters “-q 10 -l 150 --headcrop 75 -- tailcrop 75”. We assembled an initial transcriptome draft with RATTLE assembler using the filtered Nanopore reads. We then aligned filtered Illumina and Pacbio reads to the initial draft using Minimap2 (v 2.17-r941) to perform base polishing using Pilon (v 1.23). To remove chimeric transcripts or regions with poor read support, we performed a coverage scan with a rolling window size of 10 bp to trim both ends of the transcript that have less than 33% of the maximum alignment coverage. After trimming, transcripts that have lengths shorter than 300 bp were removed. We then re-mapped the Illumina reads to the initial draft using Salmon quant (v 1.3.0) and clustered similar transcripts with Grouper (https://github.com/COMBINE-lab/grouper) to remove duplicate transcripts. Illumina and Pacbio reads were then re-mapped against the clustered transcriptome using Minimap2 for a second round of base polishing, yielding the final version of the transcriptome. We predicted the open reading frame (ORF) for each transcript using TransDecoder (v 5.5.0) (https://github.com/TransDecoder/TransDecoder) with default parameters, keeping only the predicted ORF with the longest length. We performed functional annotation using Trinotate (v 3.2.1). To identify putative homologs, we performed blastx on the transcriptome against the NCBI “refseq_protein” database. To evaluate the completeness of our transcriptomes, we performed BUSCO (v 4.0.5) analysis.
Assembly: NPv6
Supplementary files format and content: 230318_light_experiment_1_Illumina_SmartSeq2_bulk_NPv6/tables/NPv6_Illumina.algae.TPM.tsv.gz : Tab-separated TPM values of algal transcripts in light exposed group.
Supplementary files format and content: 230318_light_experiment_1_Illumina_SmartSeq2_bulk_NPv6/tables/NPv6_Illumina.counts.tsv.gz : Tab-separated non-normalized counts of all transcripts in light exposed group.
Supplementary files format and content: 230318_light_experiment_1_Illumina_SmartSeq2_bulk_NPv6/tables/NPv6_Illumina.algae.counts.tsv.gz : Tab-separated non-normalized counts of algal transcripts in light exposed group.
Supplementary files format and content: 230318_light_experiment_1_Illumina_SmartSeq2_bulk_NPv6/tables/NPv6_Illumina.sample_annotation.tsv.gz : Tab-separated values of meta information for light exposed group.
Supplementary files format and content: 230318_light_experiment_1_Illumina_SmartSeq2_bulk_NPv6/tables/NPv6_Illumina.acoel.counts.tsv.gz : Tab-separated non-normalized counts of acoel transcripts in light exposed group.
Supplementary files format and content: 230318_light_experiment_1_Illumina_SmartSeq2_bulk_NPv6/tables/NPv6_Illumina.TPM.tsv.gz : Tab-separated TPM values of all transcripts in light exposed group.
Supplementary files format and content: 230318_light_experiment_1_Illumina_SmartSeq2_bulk_NPv6/tables/NPv6_Illumina.acoel.TPM.tsv.gz : Tab-separated TPM values of acoel transcripts in light exposed group.
Supplementary files format and content: 231202_231220_dpa_Illumina_SmartSeq2_bulk_NPv6/tables/NPv6_Illumina.algae.TPM.tsv.gz : Tab-separated TPM values of algal transcripts in light exposed group.
Supplementary files format and content: 231202_231220_dpa_Illumina_SmartSeq2_bulk_NPv6/tables/NPv6_Illumina.counts.tsv.gz : Tab-separated non-normalized counts of all transcripts in light exposed group.
Supplementary files format and content: 231202_231220_dpa_Illumina_SmartSeq2_bulk_NPv6/tables/NPv6_Illumina.algae.counts.tsv.gz : Tab-separated non-normalized counts of algal transcripts in light exposed group.
Supplementary files format and content: 231202_231220_dpa_Illumina_SmartSeq2_bulk_NPv6/tables/NPv6_Illumina.sample_annotation.tsv.gz : Tab-separated values of meta information for light exposed group.
Supplementary files format and content: 231202_231220_dpa_Illumina_SmartSeq2_bulk_NPv6/tables/NPv6_Illumina.acoel.counts.tsv.gz : Tab-separated non-normalized counts of acoel transcripts in light exposed group.
Supplementary files format and content: 231202_231220_dpa_Illumina_SmartSeq2_bulk_NPv6/tables/NPv6_Illumina.TPM.tsv.gz : Tab-separated TPM values of all transcripts in light exposed group.
Supplementary files format and content: 231202_231220_dpa_Illumina_SmartSeq2_bulk_NPv6/tables/NPv6_Illumina.acoel.TPM.tsv.gz : Tab-separated TPM values of acoel transcripts in light exposed group.

organism: Convolutriloba longifissura

source_name: Posterior fragment

growth_protocol: Acoels were cultured in a 16 gallon Coralife Biocube Aquarium in artificial seawater (ASW, 34 ppt, Instant Ocean) at 26 °C with a 14h:10h light:dark cycle. Acoels were fed freshly hatched Artemia shrimp every 1-3 days ad libitum in the tank. Animals used in experiments were kept in individual wells in an incubator at 26 °C with a 14:10h light:dark cycle, with filtered ASW. These animals were fed and their water was changed every 1-3 days.

extract_protocol:
Three replicates each containing five animals were used for RNA extraction for each condition. We rinsed the animals in ASW twice and then removed as much ASW as possible. 300 μl of Trizol was added, followed by a 2-3 min incubation at room temperature and vigorous vortexing to dissociate the tissue. Samples were then flash frozen on dry ice and kept at -80 °C until extraction so that all samples for each RNA-seq experiment could be processed in parallel. On the day of the extraction, samples were thawed on ice and 700 μl of fresh Trizol was added. After brief vortexing, 200 μl of chloroform was added and the sample was shaken vigorously for 15 s followed by a 2 min incubation. Samples were then centrifuged (16,000 g, 15 min at 4 °C) and the aqueous phase was carefully transferred into new tubes and processed with the Direct-zol RNA Purification Kit (Zymo Research, cat. #R2051) following the manufacturer’s instructions, which includes a DNAse treatment step. RNA concentration and quality was quantified on a Bionanalyzer.
Nextera XT library prep

treatment_protocol: Animals were kept individually or in groups smaller than 10 individuals in 12-well or 24-well plates in an incubator (Danby Fresh 1.7 cu. ft. Herb Grower, cat. #DFG17A1B). RNA were extracted from anterior or posterior fragments 0 hour or 3 hours after amputation. Double stranded RNA (dsRNA) was synthesized using pJC53.2 plasmids, and resuspended in 50 μL MilliQ water. RNAi was performed through microinjection into the gut using a XenoWorks Digital Microinjector. Needles were pulled with a vertical micropipette puller (Sutter Instruments Model P-30, with settings heat: 750 and pull: 750). The dsRNA was diluted 1:1 with ASW and mixed with food coloring dyes for visual confirmation of successful delivery. runt RNAi injections were done every 2 days over a week (3 injections total). Animals were fed brine shrimp before injections to ensure the formation of the acoel gut, and water was changed every couple of days. As the negative control, acoels were injected with the ccdB and camR insert from the pJC53.2 plasmid. Control RNAi was administered with the same frequency and for the same time span as runt respectively. After control or runt RNAi treatment, animals were amputated and only the tail fragment was kept for RNA extraction.

value: Posterior fragment

value: Runt RNAi, 0 day post-injury


title: Posterior segment, control RNAi, 2 day post-injury, replicate 3

value: control RNAi, 2 day post-injury


title: Posterior segment, Runt RNAi, 0 day post-injury, replicate 1


title: Posterior segment, control RNAi, 2 day post-injury, replicate 2


title: Posterior segment, Runt RNAi, 2 day post-injury, replicate 1

value: Runt RNAi, 2 day post-injury


title: Posterior segment, Runt RNAi, 2 day post-injury, replicate 3


title: Control1

status: Public on Apr 19 2024

city: Chongqing

first: Hang

last: Sun

address: No. 2 Tiansheng Road

institute: Southwest University

data_processing:
The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated. About 50 raw reads for each sample were generated. Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads. Then about 50 clean reads  for each sample were retained for subsequent analyses. The clean reads were mapped to the reference genome  using HISAT2. FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count. PCA analysis were performed using R (v 3.2.0) to evaluate the biological duplication of samples.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Brain

extract_protocol:
Total RNA was extracted using the TRIzol reagent  (Invitrogen, CA, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
the libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions. The transcriptome sequencing and analysis were conducted by OE Biotech Co., Ltd. (Shanghai, China).

value: Brain

value: All cells in the brain tissue

value: All cell types in brain tissue

value: WT

value: Sterile distilled water intranasal exposure, 28 days


title: Posterior segment, control RNAi, 1 day post-injury, replicate 2

value: control RNAi, 1 day post-injury


title: Posterior segment, Runt RNAi, 1 day post-injury, replicate 3

value: Runt RNAi, 1 day post-injury


title: Posterior segment, Runt RNAi, 2 day post-injury, replicate 2


title: Posterior segment, Runt RNAi, 1 day post-injury, replicate 1


title: Posterior segment, Runt RNAi, 1 day post-injury, replicate 2


title: Posterior segment, 24 hour high light exposure, replicate 3

description:
RNA-seq
light_experiment_bulk_NPv6.tar
230318_light_experiment_1_Illumina_SmartSeq2_bulk_NPv6/tables/NPv6_Illumina.algae.TPM.tsv.gz
230318_light_experiment_1_Illumina_SmartSeq2_bulk_NPv6/tables/NPv6_Illumina.counts.tsv.gz
230318_light_experiment_1_Illumina_SmartSeq2_bulk_NPv6/tables/NPv6_Illumina.algae.counts.tsv.gz
230318_light_experiment_1_Illumina_SmartSeq2_bulk_NPv6/tables/NPv6_Illumina.sample_annotation.tsv.gz
230318_light_experiment_1_Illumina_SmartSeq2_bulk_NPv6/tables/NPv6_Illumina.acoel.counts.tsv.gz
230318_light_experiment_1_Illumina_SmartSeq2_bulk_NPv6/tables/NPv6_Illumina.TPM.tsv.gz
230318_light_experiment_1_Illumina_SmartSeq2_bulk_NPv6/tables/NPv6_Illumina.acoel.TPM.tsv.gz

value: 24 hour high light exposure


title: Posterior segment, control RNAi, 2 day post-injury, replicate 1


title: Posterior segment, 3 hour high light exposure, replicate 1

value: 3 hour high light exposure


title: Posterior segment, control RNAi, 1 day post-injury, replicate 3


title: Posterior segment, Runt RNAi, 0 day post-injury, replicate 2


title: Posterior segment, control RNAi, 0 day post-injury, replicate 2

value: control RNAi, 0 day post-injury


title: Posterior segment, control RNAi, 1 day post-injury, replicate 1


title: Posterior segment, low light exposure, replicate 1

value: low light exposure


title: Posterior segment, control RNAi, 0 day post-injury, replicate 3


title: Arid1a_KO_input_ChIP_Seq

status: Public on Apr 12 2024

city: San Diego

first: Diana

middle: C.

last: Hargreaves

address: 10010 North Torrey Pines Road

institute: The Salk Institute for Biological Studies

library_source: genomic

data_processing:
Reads were aligned to the mouse genome (mm10) using STAR alignment tool (v2.5). In all cases, only reads that mapped to a unique genomic locations (MAPQ > 10) were used for downstream analysis.
HOMER (v4.8) (http://homer.salk.edu/homer/) was used to process alignment files to generate normalized bedGraphs for the UCSC Genome Browser. ChIP-seq peaks for STAT1, STAT2, and IRF9 were found by using the findPeaks program in HOMER with the default parameters for option "-style factor" using the appropriate ChIP input experiments as background.
Differential peaks were called using getDifferentialPeaksReplicates.pl (Homer) comparing WT and Arid1a -/- groups for each ChIP.
Assembly: mm10
Supplementary files format and content: bedgraph, narrowPeak (except for Input sample)

molecule: genomic DNA

source_name: MEFs

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a E220 focused-ultrasonicator (Covaris).
ChIP-seq libraries were prepared using the NEBNext Ultra II DNA library prep kit following the manufacturer's protocol.

value: MEFs

value: Mouse embryonic fibroblasts

tag: chip antibody


title: Posterior segment, 3 hour high light exposure, replicate 3

value: Posterior fragment


title: Posterior segment, control RNAi, 0 day post-injury, replicate 1


title: Posterior segment, low light exposure, replicate 3


title: Posterior segment, 3 hour high light exposure, replicate 2


title: Posterior segment, 24 hour high light exposure, replicate 2


title: Posterior segment, 24 hour high light exposure, replicate 1


title: Arid1a_KO_MEFs_rep1_RNAseq

status: Public on Apr 06 2024

data_processing:
Sequence readsSequence reads were aligned to GRCm38 (mm10) using STAR v2.5.3a (parameters- default)
RNA expression was quantified using HOMER command analyzeRepeats.pl (parameters -count exons -condenseGenes -raw)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Differential expression analysis was performed using Homer command  getDiffExpression.pl (parameters -edgeR)
Assembly: mm10
Supplementary files format and content: tab-delimited text files include normalized expression generated by edgeR or DEseq2

source_name: Arid1a fl/fl MEFs

extract_protocol:
RNA was harvested using the Zymo Research Quick-RNA MiniPrep Kit.
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Arid1a fl/fl MEFs

value: Fibroblasts

value: Arid1a -/-

value: Tamoxifen

tag: time

value: Day 5 Post Tamoxifen


title: Arid1a_KO_MEFs_rep2_RNAseq


title: Total_RNA_seq_sgArid1a_B16F10_rep1

value: Melanoma


title: Total_RNA_seq_sgArid1a_B16F10_rep2


title: Total_RNA_seq_sgScr_B16F10_rep2

value: sgScramble


title: Total_RNA_seq_sgScr_B16F10_rep1


title: WT_MEFs_rep2_RNAseq

value: WT

value: Ethanol

value: Day 5 Post EtOH


title: BD98_anti_IFNAR_B16F10_rep2_RNAseq

value: BD98 + Anti-IFNAR


title: WT_MEFs_rep1_RNAseq


title: sgScr_MC38_rep1_RNAseq

value: Colon Cancer


title: sgArid1a_MC38_rep1_RNAseq


title: BD98_anti_IFNAR_B16F10_rep1_RNAseq


title: sgScr_MC38_rep2_RNAseq


title: Posterior segment, low light exposure, replicate 2


title: BD98_B16F10_rep1_RNAseq


title: DMSO_B16F10_BD98_exp_rep2_RNAseq

value: DMSO


title: DMSO_B16F10_BD98_exp_rep1_RNAseq


title: sgArid1a_Ruxolitinib_B16F10_rep2_RNAseq

value: Ruxolitinib


title: sgScr_DMSO_JAKi_exp_B16F10_rep2_RNAseq


title: sgArid1a_Ruxolitinib_B16F10_rep1_RNAseq


title: sgArid1a_DMSO_B16F10_rep2_RNAseq


title: sgArid1a_anti_IFNAR_B16F10_rep1_RNAseq

value: Anti-IFNAR antibody


title: sgArid1a_anti_IFNAR_B16F10_rep2_RNA_seq


title: Sting_dKO_B16F10_rep2_RNAseq


title: sgArid1a_MC38_rep2_RNAseq


title: Sting_dKO_B16F10_rep1_RNAseq


title: Cgas_dKO_B16F10_rep2_RNAseq


title: sgArid1a_B16F10_rep1_RNAseq


title: sgArid1a_B16F10_rep2_RNAseq


title: sgScr_B16F10_rep2_RNAseq


title: sgArid1a_IFNg_B16F10_rep2_RNAseq

value: Murine IFN gamma


title: sgScr_B16F10_rep1_RNAseq


title: BD98_B16F10_rep2_RNAseq


title: sgArid1a_IFNg_B16F10_rep1_RNAseq


title: sgArid1a_DMSO_B16F10_rep1_RNAseq


title: sgScr_PBS_B16F10_rep2_RNAseq

value: PBS


title: sgScr_IFNg_B16F10_rep2_RNAseq


title: sgArid1a_B16F10_tumor_rep2_RNAseq

source_name: B16F10 tumor

value: B16F10 tumor

value: Subcutaneous tumor injection

value: Day 15


title: sgScr_DMSO_JAKi_exp_B16F10_rep1_RNAseq


title: sgScr_PBS_B16F10_rep1_RNAseq


title: sgScr_IFNg_B16F10_rep1_RNAseq


title: sgArid1a_B16F10_tumor_rep1_RNAseq


title: sgScr_B16F10_tumor_rep2_RNAseq


title: Cgas_dKO_B16F10_rep1_RNAseq


title: sgScr_B16F10_tumor_rep1_RNAseq


title: sgArid1a_CD8_T_cell_scRNA_rep1

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Downstream analysis of single cell gene expression and quality control was performed using Seurat R package.
Single cell TCR analysis was performed using scRepertoire R package.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: B16F10 Tumor

extract_protocol:
Tumors were dissociated by chopping followed by incubation with Liberase (Roche, 5401020001) and DNase I (Roche, 11284932001), homogenized and filtered through a 100uM filter, depleted of red blood cells via RBC lysis buffer (BioLegend, 420301), and single cell suspension obtained via centrifugation in 47% Percoll solution. CD8+ T cells were then FACS sorted by sorting CD45+ CD3+ CD8+ Viability Dye negative cells.
Library was performed according to the manufacter’s instructions (Chromium Next GEM Single Cell 5’ Reagent Kit v2 and TCR amplification kit, 10X Genomics).

value: CD8+ T cells

value: B16F10 Tumor

tag: strain

tag: age

value: 6-8 weeks old


title: sgScr_CD8_T_cell_scRNA_rep2

description: 10x Genomics


title: WT_input_ChIP_Seq

value: MEFs

value: Mouse embryonic fibroblasts


title: Arid1a_KO_MEFs_IRF9_ChIP_Seq

value: IRF9 (Millipore, #MABS1920)


title: sgArid1a_CD8_T_cell_scRNA_rep2

description: 10x Genomics


title: Arid1a_KO_MEFs_STAT2_ChIP_Seq


title: sgArid1a_PBS_B16F10_rep2_RNAseq

value: Melanoma


title: Arid1a_KO_MEFs_STAT1_ChIP_Seq


title: sgArid1a_PBS_B16F10_rep1_RNAseq


title: WT_MEFs_IRF9_ChIP_Seq


title: WT_MEFs_STAT2_ChIP_Seq


title: sgArid1a_ATAC_rep2

data_processing:
Sequence readsSequence reads were aligned to GRCm38 (mm10) using STAR v2.5.3a (parameters- default)
The 'runATAC' command in Homer (http://homer.salk.edu/homer/) was used to generate bedGraphs, BAM files, QC info, and Peak files.
Differential peak analysis was performed using getDifferentialPeaksReplicates.pl command (Homer)
Assembly: mm10
Supplementary files format and content: bedgraph, broadPeak

extract_protocol:
The Omni-ATAC protocol (Corces et al, 2017) was utilized with 50,000 cells used as input per Tn5 reaction.
ATAC-seq libraries were prepared as previously described in Corces et al, 2017 Nature Methods article: "An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues"


title: WT_MEFs_STAT1_ChIP_Seq


title: sgArid1a_ATAC_rep1


title: sgScr_ATAC_rep2


title: sgScr_ATAC_rep1


title: MCAS_25_Input_H3k4me1

status: Public on Mar 18 2024

city: Los Angeles

first: Michelle

middle: Renee

last: Jones

address: 8720 Alden Dv

department: Biomedical Sciences

institute: Cedars-Sinai Medical Center

description: ChIP-Seq for H3K4me1 with Replicate 1 (R1), Replicate 2 (R2) and Input available. Fastq provided for Replicate 1 (R1) and Replicate 2 (R2) and Input.

data_processing:
ChIP sequencing data was processed based on ENCODE phase 3 histone ChIP-Seq pipeline with modifications on the peak calling algorithm to retain peaks with p-value < 10e-9.
Reads were aligned to the reference human genome (hg38), filtered by read quality and duplicate reads removed. Peak calling was performed with MACS2 within the AQUOS pipeline, with pooled replicate peaks that overlap 50% or more of each individual replicate selected for the final peak set. When replicates were not available pseudo replicates were formed and pooled peaks selected in the same manner from these pseudo replicates. Narrowpeaks were retained for downstream analysis.
Assembly: hg38
Supplementary files format and content: narrowpeak

source_name: cell line

growth_protocol: FT33, FT246 and FT282 lines were maintained in DMEM-F12 medium (Gibco, Invitrogen, Carlsbad) supplemented with 10% fetal bovine serum (Gibco). The HGSOC cell line UWB 1.289 was cultured in a mixture (1:1) of 50% RPMI and  50% MEGM medium with 3% FBS and Kuramochi was cultured in RPMI-1640 media supplemented with 10% FBS. The remaining cell lines were maintained according to the recommended conditions (ATCC).   All cell lines were thawed and allowed to recover for 1 day before expansion. All cell lines were passaged and plated onto 150mm plates. Cells were harvested at 80% confluency to be fixed, pelleted and snap frozen.

extract_protocol:
Four 15-cm dishes of confluent cells were fixed in formaldehyde for 10 min, before quenching the fixation with glycine. Cells were collected, lysed in a sarkosyl-containing lysis buffer and sonicated  to yield 100- to 300-bp genomic DNA fragments. Five micrograms of an antibody raised against H3K4me1 was incubated with blocked magnetic Dynabeads (Life Technologies) at 4 °C for 4 h. Antibody–bead conjugates were incubated with 100 μg of chromatin at 4 °C overnight, with constant agitation. Beads were washed extensively with RIPA buffer and then treated with RNase and proteinase K (both Qiagen). DNA was then eluted from the beads in TE buffer and cleaned up using the QIAquick PCR Purification kit (Qiagen).
Sequencing libraries were prepared using a ThruPlex DNA-seq kit (Rubicon R400407), pooled and sequenced on an Illumina HiSeq 5000 for 2 x 150 bp paired-end for an average of 40 million reads (Fulgent Genetics; Temple City, CA).

value: cell line

value: MCAS

value: Mucinous serous ovarian cancer

value: H3K4me1 (Abcam ab8895)


title: EFO27_25_Input_H3k4me1


title: EFO27_A_H3k4me1


title: EFO27_B_H3k4me1


title: GTFR230_B_H3k4me1


title: GTFR230_25_Input_H3k4me1


title: sgScr_CD8_T_cell_scRNA_rep1

description: 10x Genomics


title: VOA1056_25_Input_H3k4me1

value: Low grade serous ovarian cancer


title: VOA1056_B_H3k4me1


title: GTFR230_A_H3k4me1


title: MCAS_A_H3k4me1


title: VOA1056_A_H3k4me1


title: OAW42_B_H3K4me1


title: OAW42_A_H3K4me1


title: Kuramochi_25_Input_H3k4me1

value: Kuramochi

value: High grade serous ovarian cancer


title: UWB1.289_Input_H3K4me1

description: ChIP-Seq for H3K4me1 with only bam file available. Bam provided for Replicate 1 and Replicate 2 (R2) and Input.


title: Kuramochi_A_H3k4me1


title: UWB1.289_A_H3K4me1


title: Hey_B_H3k4me1

value: Hey


title: Hey_Input_H3k4me1


title: CaOV3_B_H3K4me1


title: UWB1.289_B_H3K4me1


title: CaOV3_A_H3K4me1


title: Hey_A_H3k4me1


title: MCAS_B_H3k4me1


title: RMG-II_25_Input_H3K4me1

value: RMG-II

value: Clear cell ovarian cancer


title: RMG-II_B_H3K4me1


title: CaOV3_Input_H3K4me1


title: RMG-II_A_H3K4me1


title: JHOC5_25_Input_H3k4me1


title: ES2_25_Input_H3K4me1

description: ChIP-Seq for H3K4me1 with Replicate 1 only and Input available. Fastq provided for Replicate 1 (R1) and Input.


title: JHOC5_B_H3k4me1


title: JHOC5_A_H3K4me1


title: ES2_H3K4me1


title: FT282_Input_H3K4me1

value: Fallopian tube derived epithelial cell


title: FT282_B_H3K4me1


title: OAW42_Input_H3K4me1


title: TA muscle, non-CTX Injected, Subject 1

status: Public on Mar 08 2024

city: Berkeley

first: Alec

last: Bizieff

address: 54 Mulford Hall

institute: UC Berkeley

data_processing:
The clustering of the index-coded samples was performed on an Illumina Novaseq sequencer according to the manufacturer’s instructions. After cluster generation, the libraries were sequenced on the same machine and paired-end reads were generated.
Assembly: mm10
Supplementary files format and content: CTX_Genes.xlsx

source_name: Tibialis Anterior

extract_protocol:
Whole RNA transcripts were isolated from frozen purified muscle fibers, according to manufacturer's instructions (Qiagen RNA Extraction Mini Kit, #74104)
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. To select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37 °C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: CTX-treated groups received a dose of 50 µL 0.1mg/mL CTX in sterile PBS/0.2% Meloxicam in the form of an intramuscular injection in the Tibialis Anterior (TA) muscle to one limb while the TA from the other limb was not injected. One group of mice did not receive CTX injection to serve as uninjured controls but did receive 3 days of stable isotope labeling alongside experimental groups.

value: Tibialis Anterior

value: Bulk Tissue

value: Non-CTX Injected


title: TA muscle, non-CTX Injected, Subject 2


title: TA muscle, non-CTX Injected, Subject 3


title: FT282_A_H3K4me1


title: TA muscle, Maturation Group, CTX Injected, Subject 4

value: CTX Injected


title: Kuramochi_B_H3k4me1


title: TA muscle, Maturation Group, CTX Injected, Subject 3


title: TA muscle, Maturation Group, CTX Injected, Subject 2


title: TA muscle, Differentiation Group, CTX Injected, Subject 3


title: TA muscle, Proliferation Group, CTX Injected, Subject 4


title: TA muscle, Differentiation Group, CTX Injected, Subject 4


title: TA muscle, Differentiation Group, CTX Injected, Subject 1


title: TA muscle, Proliferation Group, CTX Injected, Subject 1


title: TA muscle, Proliferation Group, CTX Injected, Subject 3


title: TA muscle, Differentiation Group, CTX Injected, Subject 2


title: RBM10-Flag IP-seq rep3

city: LOS ANGELES

first: Chia-ho

last: Lin

address: 6577 MRL. 675 CHARLES E YOUNG DR. SOUTH

institute: UCLA

description:
selective U2 snRNA degradation
insert length 28-55 nt
Barcode: GTT

data_processing:
3’ adapter were trimmed using Cutadapt (cutadapt -a TGAGATCGGAAGAGCGGTTCAG -m 28 -e 0.2 -u 4 --max n 5)
Trimmed sequencing were splitted by sample barcodes using FASTX. PCR diplicated were removed using in-house pipeline.
Sequencing reads were then maped to hg19 using Bowtie2 (--very sensitive -N 1 -p 5 -L12 --end-to-end --no-unal)
bigwig files were generated using the RSeQc bam2wig.py function.
Assembly: hg19
Supplementary files format and content: bigwig
Supplementary files format and content: branch_site_peak_intensity.xlsx: branch site peak intensity.
Supplementary files format and content: predicted_BP.xlsx: predicted branch point.

source_name: 293Flp-In cells

growth_protocol: HMW extracts with TDNase+RNasaA+RNaseT1+Benzonase.

extract_protocol:
RNP-seq, IP-seq, 10-22 PCR cycles.
The reads from these libraries look as follows:   NNNNabcNNNNxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxTGAGATCGGAAGAGCGGTTCAG   Where   - NNNN is a four nucleotide degenerate sequence region. The first to these is to ensure high complexity sequence at the beginning, and the second - to serve as a reference for removing PCR duplications.   - abc is a three letter barcode:  - xxxxxxxxxxxxxxxxxxxxxx...xxxxxxxx denotes the RNA fragmnet insert in the read. The insert starts at position 12 (1-based) of the read, and originate from human (HEK293) RNA fragments 28-70 nt in length.   - The TGAGATCGGAAGAGCGGTTCAG sequence is common for all reads and should be immediately downstream of the insert.

value: 293Flp-In cells

value: HMW nuclear extract


title: RBM10-Flag IP-seq rep2

description:
selective U2 snRNA degradation
insert length 28-55 nt
Barcode: CTG


title: RBM10-Flag IP-seq rep1

description:
selective U2 snRNA degradation
insert length 28-55 nt
Barcode: AGA


title: SF3A3-Flag IP-seq rep3

description:
selective U2 snRNA degradation
insert length 28-55 nt
Barcode: ATC


title: SF3A3-Flag IP-seq rep1

description:
selective U2 snRNA degradation
insert length 28-55 nt
Barcode: AAG

value: HMW nuclear extract, gradient fraction 11-13


title: RBM5-Flag RNP-seq rep3


title: RBM5-Flag RNP-seq

description:
U2 snRNA not digested
insert length 25-80 nt
Barcode: CAT


title: SF3A3-Flag IP-seq rep2


title: SF3A3-Flag RNP-seq rep3


title: RBM5-Flag RNP-seq rep2

description:
selective U2 snRNA degradation
insert length 28-55 nt
Barcode: GGG


title: RBM5-Flag RNP-seq rep1


title: SF3A3-Flag RNP-seq rep1


title: SF3A3-Flag RNP-seq rep2

description:
selective U2 snRNA degradation
insert length 28-55 nt
Barcode: CAT


title: SYN-Cre Naïve GFP+

status: Public on Mar 01 2024

city: Bronx

first: Jelena

last: Radulovic

state: NY

address: 1410 Pelham Parkway South

department: Neuroscience

institute: Albert Einstein College of Medicine

description: 10x Genomics

data_processing:
Cell Ranger Pipeline v7.0.1
Assembly: mm10
Supplementary files format and content: HDF5 Feature Barcode Matrix Format

molecule: nuclear RNA

source_name: dorsal hippocampus

extract_protocol:
Fresh dorsal hippocampal tissue was collected from mice 96 h after contextual fear conditioning (CFC). RNase inhibitor was added to the 6x Homogenization Buffer Stable Master Mix (30 mM CaCl2, 18 mM Mg(Ac)2, 60 mM Tris pH 7.8, in H2O) at a final concentration of 1.2U/μl. Tissue was homogenized using a Polytron homogenizer for 1.5 minutes. Samples were resuspended with the 50% iodixanol solution (50% iodixanol in 1× homogenization buffer) via gentle pipetting to make a final concentration of 25% iodixanol. 3ml of a 35% iodixanol solution (35% iodixanol in 1× homogenization containing 480 mM sucrose) was added to a new 15 ml Falcon tube. 3ml of a 29% iodixanol solution (29% iodixanol in 1× homogenization buffer containing 480 mM sucrose) was layered above the 35% iodixanol mixture. A 4ml 25% iodixanol solution was layered on the 29% solution. In a swinging-bucket centrifuge, nuclei were centrifuged for 20 min at 3,000 r.c.f. After centrifugation, the nuclei were present at the interface of the 29% and 35% iodixanol solutions. This band with the nuclei was collected in a 300 μl volume and transferred to a pre-chilled tube. Following isolation, nuclei were counted and resuspend in FACs buffer (1% BSA, 1mM EDTA, and 0.2U/μl RNase inhibitor in PBS) at 2 million nuclei per milliliter. A subset of nuclei was sorted by GFP expression on a high-speed cell sorter flow cytometer (Beckman Coulter MoFlowXDP cell sorter).
snRNA-seq libraries were generated from up to 10,000 individual cells captured in an oil emulsion on a Chromium Controller (10x Genomics, Pleasanton, CA.) cDNA wasgenerated in the individual cell-gel bead emulsion micro-reactors while adding barcodes at the cellular and molecular level using the Chromium Next GEM Single Cell 3' Kit v3.1(10xGenomics kit 1000268.) The barcoded cDNAs from the individual cells were combined for the remaining library process. The unique molecular barcodes (UMIs) prevented amplification artifacts to skew the analysis. The libraries were analyzed on a Fragment Analyzer 5200 (Agilent Technologies, Santa Clara, CA) to ensure a normal sizedistribution with an average size of 450 bp and sequenced on an llumina Sequencer with the following read lengths: 28 bp for Read 1, 10bp for i7 Index,10bp for i5 Index and 90 bp forRead 2 at a read depth of 20,000 reads per cell.

value: dorsal hippocampus

value: Cre


title: SYN-Cre Naïve GFP-

description: 10x Genomics


title: SYN-GFP Naïve

description: 10x Genomics


title: TA muscle, Maturation Group, CTX Injected, Subject 1


title: SYN-GFP CFC

description: 10x Genomics

value: CFC


title: SYN-Cre CFC

description: 10x Genomics

value: Cre + CFC


title: scRNAseq librairy of isolated ABD and GF adipose tissue SVF of female#5

status: Public on Feb 23 2024

city: orlando

first: Adeline

last: Divoux

state: FL

address: 301 E. Princeton St

department: Translational Research Institute

institute: Adventhealth

data_processing:
FASTQ files are processed with the CogentAP pipeline using appropriate sample WellList.TXT files. Due to two samples with primer A and primer B sex indexes being sequenced on the same pair-end sequencing lane, each pair of FASTQ files will be processed through cogentAP twice, once with the first sample wellList.TXT file and secondly with the second sample WellList.TXT file.
Following trimming, data was aligned to the GRCh19 reference genome and sample count matrices were generated that contain counts for all the single nuclei analyzed for that sample
Assembly: GRCh19
Supplementary files format and content: CSV files include raw read count values  all the single nuclei profiles for that sample

source_name: adipose tissue

extract_protocol:
SVF was isolated from ABD and GF-adipose tissue biopsies tissue was digested with collagenase (type 1, 1 mg/ml in HBSS) for 45min at 37ºC with shaking (100 rpm). The mixture was centrifuged at 500g for 5 minutes and floating adipocytes were discarded. Cell pellets were treated with erythrocyte lysis buffer (Invitrogen) for 5 min at room temperature. After discarding the supernatant, cells were repelleted with centrifugation, resupend in PBS/EDTA and the mixture was passed through 100 and 40 micron mesh filters. After centrifugation, the cells were resuspended in PBS/10% FBS/1%EDTA and counted with a Countess II automated cell counter (Thermofisher Scientific). SVF were isolated from 5 healthy women (38yo ±4.4; 31.8kg/m-2 ±3.12; WHR 0.86 ±0.05).  Single cell suspension (56K/mL) was distributed into eight wells of a 384-well source plate (Takara Bio USA, San Jose, CA) and dispensed onto a iCELL8 350v Chip (Takara Bio USA) using an iCELL8 MultiSample NanoDispenser (Takara Bio USA). We distributed the ABD and GF-SVF of each subject on the same chip.
Selected cells were subjected to first-strand cDNA synthesis initiated by oligo dT primer (SMART-Seq ICELL8 CDS), followed by template switching with template switching oligo (SMART-Seq ICELL8 oligonucleotide) for 2nd strand cDNA synthesis, prior to unbiased amplification of full-length cDNA. Synthesized full-length cDNA was tagmented by TDE1 (Illumina Tagment DNA enzyme) and amplified using forward (i5) and reverse (i7) indexing primers. Each single nucleus was indexed by a unique combination of 1 of 72 forward and 1 of 72 reverse indexing primers allowing for downstream identification. Collected cDNA was purified twice using a 1:1 proportion of AMPure XP beads (Beckman, A63880), further amplified according to manufacturer’s instructions and purified again at a 1:1 proportion of AMPure XP beads. The resultant sequencing-ready cDNA library was assessed for concentration by fluorometer (Qubit) and quality by electrophoresis (Agilent Bioanalyzer high sensitivity DNA chips) respectively. Libraries were sequenced with Illumina HiSeqX.

value: adipose tissue

tag: Sex

value: female

value: stoma vascular fraction


title: scRNAseq librairy of isolated ABD and GF adipose tissue SVF of female#4


title: TA muscle, Proliferation Group, CTX Injected, Subject 2


title: scRNAseq librairy of isolated ABD and GF adipose tissue SVF of female#2


title: scRNAseq librairy of isolated ABD and GF adipose tissue SVF of female#1 & female#3


title: Sonicate fluid 88 [983]

status: Public on Feb 19 2024

city: Rochester

first: Aditya

last: Bhagwate

address: 200 1st Street SW

institute: Mayo Clinic

data_processing:
Reads were aligned to the hg38 genome using Tophat2
Gene and exon counts were generated using FeatureCounts
Assembly: hg38
Supplementary files format and content: gene_counts.txt (Gene Expression Counts)

source_name: Knee/Hip

extract_protocol:
Total RNA was extracted from sonicate fluid samples using the miRNeasy Serum/Plasma kit (QIAGEN, Germantown, MD) and analyzed for quantity and integrity using a Qubit® 2.0 Fluorometer (Thermo Fisher Scientific, Coon Rapids, MN) coupled with the Qubit RNA high-sensitive assay kit, and a 4200 TapeStation system (Agilent, Santa Clara, CA), respectively.
RNA was treated with DNase (QIAGEN) and a Ribo-Zero rRNA removal kit (Bacteria) to remove genomic DNA and bacterial ribosomal RNA (rRNA). To prepare sequencing libraries, the Ovation SoLo RNA-Seq System (NuGEN Technologies) was used with 1 ng of RNA input. In addition, External RNA Control Consortium (ERCC) RNA Spike-In Mix 1 (Thermo Fisher Scientific)  was added as a control for library preparation and sequencing, according to the manufacturer’s recommendations. The library construction process also included a human-specific rRNA depletion step that involved adding a custom-designed Solo AnyDeplete probe mix (NuGEN Technologies) after initial cDNA synthesis and amplification
Sequencing was performed on an Illumina HiSeq 4000 instrument with 10 samples multiplexed per lane, with paired-end read and 100 cycle settings

value: Knee/Hip

value: Sonicate fluid


title: Sonicate fluid 91 [995]


title: Sonicate fluid 90 [990]


title: Sonicate fluid 92 [996]


title: Sonicate fluid 93 [997]


title: Sonicate fluid 89 [987]


title: Sonicate fluid 87 [982]


title: Sonicate fluid 81 [927]


title: Sonicate fluid 80 [904]


title: Sonicate fluid 82 [933]


title: Sonicate fluid 77 [883]


title: Sonicate fluid 85 [972]


title: Sonicate fluid 76 [881]


title: Sonicate fluid 83 [936]


title: Sonicate fluid 75 [870]


title: Sonicate fluid 74 [854]


title: Sonicate fluid 84 [95]


title: Sonicate fluid 73 [825]


title: Sonicate fluid 79 [899]


title: Sonicate fluid 72 [818]


title: Sonicate fluid 70 [786]


title: Sonicate fluid 78 [894]


title: Sonicate fluid 69 [773]


title: Sonicate fluid 68 [770]


title: Sonicate fluid 71 [792]


title: Sonicate fluid 66 [754]


title: Sonicate fluid 86 [978]


title: Sonicate fluid 64 [713]


title: Sonicate fluid 62 [706]


title: Sonicate fluid 63 [709]


title: Sonicate fluid 61 [696]


title: Sonicate fluid 58 [658]


title: Sonicate fluid 57 [638]


title: Sonicate fluid 56 [635]


title: Sonicate fluid 51 [42]


title: Sonicate fluid 52 [461]


title: Sonicate fluid 53 [47]


title: Sonicate fluid 67 [769]


title: Sonicate fluid 49 [312]


title: Sonicate fluid 47 [293]


title: Sonicate fluid 44 [262]


title: Sonicate fluid 48 [299]


title: Sonicate fluid 45 [283]


title: Sonicate fluid 46 [292]


title: Sonicate fluid 43 [219]


title: Sonicate fluid 40 [186]


title: Sonicate fluid 38 [159]


title: Sonicate fluid 65 [725]


title: Sonicate fluid 41 [197]


title: Sonicate fluid 42 [199]


title: Sonicate fluid 37 [1364]


title: Sonicate fluid 39 [163]


title: Sonicate fluid 60 [692]


title: Sonicate fluid 59 [659]


title: Sonicate fluid 35 [1337]


title: Sonicate fluid 33 [1333]


title: Sonicate fluid 32 [1323]


title: Sonicate fluid 36 [1354]


title: Sonicate fluid 54 [50]


title: Sonicate fluid 55 [593]


title: Sonicate fluid 31 [1302]


title: Sonicate fluid 30 [1285]


title: Sonicate fluid 50 [415]


title: Sonicate fluid 29 [1277]


title: Sonicate fluid 28 [1270]


title: Sonicate fluid 27 [1244]


title: Sonicate fluid 22 [1171]


title: Sonicate fluid 24 [1208]


title: Sonicate fluid 26 [1242]


title: Sonicate fluid 21 [1161]


title: Sonicate fluid 20 [116]


title: Sonicate fluid 23 [1197]


title: Sonicate fluid 17 [1069]


title: Sonicate fluid 16 [1068]


title: Sonicate fluid 13 [1061]


title: Sonicate fluid 15 [1067]


title: Sonicate fluid 10 [1039]


title: Sonicate fluid 19 [1100]


title: Sonicate fluid 14 [1063]


title: Sonicate fluid 34 [1336]


title: Sonicate fluid 11 [1048]


title: Sonicate fluid 18 [1093]


title: Sonicate fluid 7 [1024]


title: Sonicate fluid 8 [1030]


title: Sonicate fluid 9 [1036]


title: Sonicate fluid 4 [1013]


title: Sonicate fluid 12 [1049]


title: Sonicate fluid 5 [1019]


title: Sonicate fluid 3 [1007]


title: Sonicate fluid 25 [122]


title: Sonicate fluid 2 [1006]


title: Sonicate fluid 6 [1021]


title: Sonicate fluid 1 [1005]


title: LCMV-Docile, replicate 2, scATAC-seq

status: Public on Feb 17 2024

city: Clayton

first: Kim

last: Good-Jacobson

state: Victoria

address: Gr Fl Reception (Bldg 77) 23 Innovation Walk

country: Australia

institute: Monash University

library_source: genomic single cell

data_processing:
The raw fastq data for each sample were processed using the 10X genomics Cell Ranger ATAC v2.0.0 pipeline, using the 'cellranger-atac count' function with defult parameters for read filtering and alignment, barcode counting, identification of transposase cut sites, detection of accessible chromatin peaks, and cell calling.
Further processing was done with Seurat v4.1.0 and Signac V1.5.
Assembly: mm10
Supplementary files format and content: hd5 file with peak matrics.
Supplementary files format and content: fragments.tsv files produced by cellranger-atac.
Supplementary files format and content: filtered_peak_bc_matrix.h5: hd5 file with peak matrices
Supplementary files format and content: fragments.tsv.gz: a bed-like file containing fragment locations and the cell barcode the fragment is assigned to.
Supplementary files format and content: fragments.tsv.gz.tbi: an index to the fragments.tsv.gz file.
Supplementary files format and content: singlecell.csv: a meta-data csv file containing QC information for each cell.

source_name: Spleen

extract_protocol:
C57Bl6 mice were infected with LCMV-WE or LCMV-Docile. 28 days after infection, spleens were surgically removed from culled mice and non-RBC splenocytes were isolated. LCMV-specific B cells were magnetically enriched using an LCMV-NP tetramer system. Enriched cells were then stained with viability dye (FVS) and relevant antibodies, and 100,000 LCMV-specific B cells per sample were sorted using the BD Influx (BD Biosciences) cell sorter.
Nuclei isolation, barcoding and library preparation were performed according to the manufacturer’s protocol using the Chromium Next GEM Single Cell ATAC Reagent Kit v1.1 (10X Genomics). Libraries were prepared using the MGIEasy v3 chemistry kit and sequenced using the MGITech MGISEQ2000RS sequencer (MGI Tech).

treatment_protocol: Infection with lymphocytic choriomeningitis virus (LCMV) (WE or Docile strain) for 28 days

value: Spleen

value: 28 days post-infection

value: LCMV-specific B cells

tag: disease state

value: Chronic infection

value: LCMV-Docile


title: LCMV-WE, replicate 1, scATAC-seq

value: Acute infection

value: LCMV-WE


title: LCMV-WE, replicate 2, scATAC-seq


title: mitoT-EC-rep2

status: Public on Feb 15 2024

city: Boston

first: Yonglin

last: Zhu

state: MA

address: 300 Longwood Ave

department: Cardiac Surgery

institute: Boston Children's Hospital

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. The hit counts were summarized and reported using the gene_id feature in the annotation file.
Assembly: Homo sapiens GRCh38
Supplementary files format and content: tab-delimited text files include count  values for all samples
Supplementary files format and content: tab-delimited text files include TPM values for all samples

extract_protocol:
Total RNA was extracted from fresh frozen cell pellet samples using Qiasymphony RNA kit following manufacturer’s instructions (Qiagen, Hilden, Germany).
RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina using the manufacturer’s instructions (NEB, Ipswich, MA, USA).

value: cell line

value: ECFC

value: Primary endothelial cells

value: WT

value: mitochondria transfer


title: unprimed-EC-rep1

value: unprimed


title: mitoT-EC-rep3


title: unprimed-EC-rep2


title: mitoT-EC-rep1


title: mitoAT-EC-rep2


title: Lymph node sample 302; GEX

status: Public on Jan 28 2024

city: Düsseldorf

first: Sascha

last: Dietrich

address: Moorenstr. 5

department: Hematology

country: Germany

institute: University Hospital Düsseldorf

description:
10xgenomics
LN0302_3'RNA

data_processing:
The demultiplexing, barcode processing, gene and epitope counting were performed using CellRanger Software v6.1.1.
Assembly: hg19
Supplementary files format and content: Processed data files of gene expression and epitope libraries are space-delimited count matrices of features versus cells (barcodes). Count matrices were filtered for T-cells.
Library strategy: CITE-Seq

source_name: Lymph node

extract_protocol:
Lymph node cells were isolated as previously described (PMID: 34746869). Briefly, whole lymph nodes were cut into small pieces of approximately 1–2 mm size. LN cells were gently washed out by rinsing the pieces several times. After centrifugation, cells were frozen until further analysis.
Gene expression and epitope libraries were performed according to the manufacturer's instructions (Chromium Next GEM Single Cell 3' Kit v3.1). TotalSeqA antibodyes were purchased from Biolegend.

value: Lymph node

value: Lymphocytes

tag: library type

value: mRNA


title: mitoAT-EC-rep1


title: Lymph node sample 295; ADT

description:
10xgenomics
LN0295_ADT

library_source: other

molecule: protein

value: ADT


title: Lymph node sample 310; GEX

description:
10xgenomics
LN0310_3'RNA


title: Lymph node sample 310; ADT

description:
10xgenomics
LN0310_ADT


title: Lymph node sample 302; ADT

description:
10xgenomics
LN0302_ADT


title: Lymph node sample 285; GEX

description:
10xgenomics
LN0285_3'RNA


title: Lymph node sample 295; GEX

description:
10xgenomics
LN0295_3'RNA


title: Lymph node sample 285; ADT

description:
10xgenomics
LN0285_ADT


title: Lymph node sample 281; ADT

description:
10xgenomics
LN0281_ADT


title: Lymph node sample 278; GEX

description:
10xgenomics
LN0278_3'RNA


title: Lymph node sample 274; GEX

description:
10xgenomics
LN0274_3'RNA


title: Lymph node sample 280; GEX

description:
10xgenomics
LN0280_3'RNA


title: Lymph node sample 280; ADT

description:
10xgenomics
LN0280_ADT


title: unprimed-EC-rep3


title: LCMV-Docile, replicate 1, scATAC-seq

value: Spleen


title: Lymph node sample 272; GEX

description:
10xgenomics
LN0272_3'RNA


title: Lymph node sample 272; ADT

description:
10xgenomics
LN0272_ADT


title: Lymph node sample 278; ADT

description:
10xgenomics
LN0278_ADT


title: Lymph node sample 266; GEX

description:
10xgenomics
LN0266_3'RNA


title: Lymph node sample 271; GEX

description:
10xgenomics
LN0271_3'RNA


title: Lymph node sample 273; GEX

description:
10xgenomics
LN0273_3'RNA


title: Lymph node sample 271; ADT

description:
10xgenomics
LN0271_ADT


title: Lymph node sample 274; ADT

description:
10xgenomics
LN0274_ADT


title: Lymph node sample 267; GEX

description:
10xgenomics
LN0267_3'RNA


title: Lymph node sample 273; ADT

description:
10xgenomics
LN0273_ADT


title: Lymph node sample 267; ADT

description:
10xgenomics
LN0267_ADT


title: Lymph node sample 262; GEX

description:
10xgenomics
LN0262_3'RNA


title: Lymph node sample 265; GEX

description:
10xgenomics
LN0265_3'RNA


title: Lymph node sample 229; ADT

description:
10xgenomics
LN0229_ADT


title: Lymph node sample 262; ADT

description:
10xgenomics
LN0262_ADT


title: Lymph node sample 251; ADT

description:
10xgenomics
LN0251_ADT


title: Lymph node sample 229; GEX

description:
10xgenomics
LN0229_3'RNA


title: Lymph node sample 228; GEX

description:
10xgenomics
LN0228_3'RNA


title: Lymph node sample 266; ADT

description:
10xgenomics
LN0266_ADT


title: Lymph node sample 217; GEX

description:
10xgenomics
LN0217_3'RNA


title: Lymph node sample 265; ADT

description:
10xgenomics
LN0265_ADT


title: Lymph node sample 217; ADT

description:
10xgenomics
LN0217_ADT


title: Lymph node sample 281; GEX

description:
10xgenomics
LN0281_3'RNA


title: Lymph node sample 210; GEX

description:
10xgenomics
LN0210_3'RNA


title: Lymph node sample 259; ADT

description:
10xgenomics
LN0259_ADT


title: Lymph node sample 211; ADT

description:
10xgenomics
LN0211_ADT


title: Lymph node sample 228; ADT

description:
10xgenomics
LN0228_ADT


title: Lymph node sample 251; GEX

description:
10xgenomics
LN0251_3'RNA


title: Lymph node sample 210; ADT

description:
10xgenomics
LN0210_ADT


title: Lymph node sample 211; GEX

description:
10xgenomics
LN0211_3'RNA


title: Lymph node sample 198; GEX

description:
10xgenomics
LN0198_3'RNA


title: Lymph node sample 179; GEX

description:
10xgenomics
LN0179_3'RNA


title: Lymph node sample 198; ADT

description:
10xgenomics
LN0198_ADT


title: Lymph node sample 186; ADT

description:
10xgenomics
LN0186_ADT


title: Lymph node sample 188; GEX

description:
10xgenomics
LN0188_3'RNA


title: Lymph node sample 193; GEX

description:
10xgenomics
LN0193_3'RNA


title: Lymph node sample 186; GEX

description:
10xgenomics
LN0186_3'RNA


title: Lymph node sample 259; GEX

description:
10xgenomics
LN0259_3'RNA


title: Lymph node sample 193; ADT

description:
10xgenomics
LN0193_ADT


title: Lymph node sample 178; GEX

description:
10xgenomics
LN0178_3'RNA


title: Lymph node sample 176; ADT

description:
10xgenomics
LN0176_ADT


title: Lymph node sample 166; GEX

description:
10xgenomics
LN0166_3'RNA


title: Lymph node sample 152; GEX

description:
10xgenomics
LN0152_3'RNA


title: Lymph node sample 176; GEX

description:
10xgenomics
LN0176_3'RNA


title: Lymph node sample 166; ADT

description:
10xgenomics
LN0166_ADT


title: Lymph node sample 179; ADT

description:
10xgenomics
LN0179_ADT


title: Lymph node sample 152; ADT

description:
10xgenomics
LN0152_ADT


title: Lymph node sample 178; ADT

description:
10xgenomics
LN0178_ADT


title: Lymph node sample 135; GEX

description:
10xgenomics
LN0135_3'RNA


title: Lymph node sample 135; ADT

description:
10xgenomics
LN0135_ADT


title: Lymph node sample 144; GEX

description:
10xgenomics
LN0144_3'RNA


title: Lymph node sample 132; GEX

description:
10xgenomics
LN0132_3'RNA


title: Lymph node sample 132; ADT

description:
10xgenomics
LN0132_ADT


title: Lymph node sample 118; GEX

description:
10xgenomics
LN0118_3'RNA


title: Lymph node sample 110; GEX

description:
10xgenomics
LN0110_3'RNA


title: Lymph node sample 118; ADT

description:
10xgenomics
LN0118_ADT


title: Lymph node sample 107; GEX

description:
10xgenomics
LN0107_3'RNA


title: Lymph node sample 188; ADT

description:
10xgenomics
LN0188_ADT


title: Lymph node sample 110; ADT

description:
10xgenomics
LN0110_ADT


title: Lymph node sample 97; GEX

description:
10xgenomics
LN0097_3'RNA


title: Lymph node sample 100; ADT

description:
10xgenomics
LN0100_ADT


title: Lymph node sample 100; GEX

description:
10xgenomics
LN0100_3'RNA


title: Lymph node sample 87; ADT

description:
10xgenomics
LN0087_ADT


title: Lymph node sample 87; GEX

description:
10xgenomics
LN0087_3'RNA


title: Lymph node sample 97; ADT

description:
10xgenomics
LN0097_ADT


title: Lymph node sample 144; ADT

description:
10xgenomics
LN0144_ADT


title: Lymph node sample 80; GEX

description:
10xgenomics
LN0080_3'RNA


title: Lymph node sample 70; GEX

description:
10xgenomics
LN0070_3'RNA


title: Lymph node sample 80; ADT

description:
10xgenomics
LN0080_ADT


title: Lymph node sample 78; ADT

description:
10xgenomics
LN0078_ADT


title: Lymph node sample 70; ADT

description:
10xgenomics
LN0070_ADT


title: Lymph node sample 60; GEX

description:
10xgenomics
LN0060_3'RNA


title: Lymph node sample 60; ADT

description:
10xgenomics
LN0060_ADT


title: Lymph node sample 53; GEX

description:
10xgenomics
LN0053_3'RNA


title: Lymph node sample 78; GEX

description:
10xgenomics
LN0078_3'RNA


title: Lymph node sample 53; ADT

description:
10xgenomics
LN0053_ADT


title: Lymph node sample 50; GEX

description:
10xgenomics
LN0050_3'RNA


title: Lymph node sample 50; ADT

description:
10xgenomics
LN0050_ADT


title: Lymph node sample 43; GEX

description:
10xgenomics
LN0043_3'RNA


title: Lymph node sample 43; ADT

description:
10xgenomics
LN0043_ADT


title: Lymph node sample 30; GEX

description:
10xgenomics
LN0030_3'RNA


title: Lymph node sample 25; ADT

description:
10xgenomics
LN0025_ADT


title: Lymph node sample 30; ADT

description:
10xgenomics
LN0030_ADT


title: Lymph node sample 107; ADT

description:
10xgenomics
LN0107_ADT


title: Lymph node sample 25; GEX

description:
10xgenomics
LN0025_3'RNA


title: Lymph node sample 14; ADT

description:
10xgenomics
LN0014_ADT


title: Lymph node sample 14; GEX

description:
10xgenomics
LN0014_3'RNA


title: Lymph node sample 417, TCR

data_processing:
The demultiplexing, barcode processing, gene counting and T-cell receptor counting were performed using CellRanger Software v6.1.1.
Assembly: hg19
Supplementary files format and content: Processed data files of gene expression libraries are tab-delimited count matrices of genes versus cells (barcodes). Count matrices were filtered for T-cells.
Supplementary files format and content: Processed data files of T-cell receptor libraries are comma-separated tables that show T-cell receptor sequences, clonotypes, etc. of T-cells (barcodes)

extract_protocol:
Lymph node cells were isolated as previously described (PMID: 34746869). Briefly, whole lymph nodes were cut into small pieces of approximately 1–2 mm size. LN cells were gently washed out by rinsing the pieces several times. After centrifugation, cells were frozen until further analysis.
Gene expression and T-cell receptor libraries were performed according to the manufacturer's instructions (Chromium Next GEM Single Cell 5ʹ Kit v2, Chromium Single Cell Human TCR Amplification Kit)

value: TCR


title: Lymph node sample 2; GEX

description:
10xgenomics
LN0002_3'RNA


title: Lymph node sample 417, GEX


title: Lymph node sample 302, TCR


title: Lymph node sample 278, GEX


title: Lymph node sample 2; ADT

description:
10xgenomics
LN0002_ADT


title: Lymph node sample 343, TCR


title: Lymph node sample 259, TCR


title: Lymph node sample 278, TCR


title: Lymph node sample 264, TCR


title: Lymph node sample 249, GEX


title: Lymph node sample 243, GEX


title: Lymph node sample 217, TCR


title: Lymph node sample 217, GEX


title: Lymph node sample 198, TCR


title: Lymph node sample 193, GEX


title: Lymph node sample 198, GEX


title: Lymph node sample 193, TCR


title: Lymph node sample 302, GEX


title: Lymph node sample 343, GEX


title: Lymph node sample 178, GEX


title: Lymph node sample 144, TCR


title: Lymph node sample 104, TCR


title: Lymph node sample 132, TCR


title: Lymph node sample 110, GEX


title: Lymph node sample 144, GEX


title: Lymph node sample 78, TCR


title: Lymph node sample 264, GEX


title: Lymph node sample 132, GEX


title: Lymph node sample 259, GEX


title: Lymph node sample 249, TCR


title: Lymph node sample 104, GEX


title: Lymph node sample 243, TCR


title: non-malignant gastric mucosa [G55N]

status: Public on Jan 19 2024

city: Fukuoka

first: Chikanori

last: Tsutsumi

address: 3-1-1 Maidashi, Higashi-ku

department: Department of Surgery and Oncology, Graduate School of Medical Sciences

country: Japan

institute: Kyushu University

data_processing:
Raw sequencing reads were aligned to the human reference genome GRCh38 and processed to a matrix representing the UMI’s per cell barcode per gene using Cell Ranger v5.0.0 (10x Genomics)
Output files were analyzed with the R v3.6.3 package "Seurat v3.1.5".
Assembly: GRCh38
Supplementary files format and content: To merge the data of all samples, we used the "SCTransform" package for the normalization and variance stabilization of molecular count data.

extract_protocol:
Single-cell library preparation was performed according to the manual of the Chromium Next GEM Single-cell 3' Reagent Kits v3.1. The cell suspensions were loaded on the Single-cell G Chip for gel bead-in-emulsion (GEM) generation and barcoding, aiming to recover 10,000 cells per sample. cDNA library thus was generated with a droplet-based sequencing platform (10X Genomics). Next, reverse transcription, RT cleanup cDNA amplification, and quantification was performed to construct a 3’ gene library.
The libraries were sequenced on NovaSeq6000 (Illumina) or DNBSEQ-G400 (MGI Tech).

tag: organ

value: stomach

tag: gender

value: Male

value: non-malignant gastric mucosa


title: Lymph node sample 78, GEX


title: non-malignant gastric mucosa [G54N]

value: Female


title: gastric cancer-Chemotherapy+Anti-PD1 [G65T]

data_processing:
Raw sequencing reads were aligned to the human reference genome GRCh38 and processed to a matrix representing the UMI’s per cell barcode per gene using Cell Ranger v5.0.0 (10x Genomics)
Output files were analyzed with the R v3.6.3 package "Seurat v3.1.5".
Supplementary files format and content: To merge the data of all samples, we used the "SCTransform" package for the normalization and variance stabilization of molecular count data.

extract_protocol:
Single-cell library preparation was performed according to the manual of the Chromium Next GEM Single-cell 3' Reagent Kits v3.1. The cell suspensions were loaded on the Single-cell G Chip for gel bead-in-emulsion (GEM) generation and barcoding. cDNA library thus was generated with a droplet-based sequencing platform (10X Genomics). Next, reverse transcription, RT cleanup cDNA amplification, and quantification was performed to construct a 3’ gene library.
The libraries were sequenced on NovaSeq6000 (Illumina) or DNBSEQ-G400 (MGI Tech).

value: gastric cancer-Chemotherapy+Anti-PD1


title: non-malignant gastric mucosa [G42N]


title: gastric cancer [G47T]

value: gastric cancer


title: non-malignant gastric mucosa [G41N]


title: Lymph node sample 178, TCR


title: OvCa1039

status: Public on Dec 15 2023

city: Dallas

first: Bingqing

last: Xie

state: Texas

address: 6001 Forest Park Rd

department: Internal medicine

institute: University of Texas Southwestern medical center

description: Dropseq

data_processing:
Barcode and umi were extracted by umi_tools 0.5.1
Allows for proportion of 0.1 mismatches (e.g. 10*0.1=1 mismatch in 10bp adaptor match, bp below zero are rounded to 0) and sequences to match are poly at the 3 prime end (at least 6) and TSO oligo on the 5 prime end via cutadapt
Alignment with STAR(2.6.1) using defaults and Assign reads to genes using featureCounts
Sort gene reads and index using samtools 1.7.0
Generate gene DGE matrix using umi_tools
Filter low quality cells with less than 400 genes per cell and mitochondria pecentage more than 25 using Seurat V4.1.3
Assembly: hg38
Supplementary files format and content: tab-delimited text files include count values for each Sample

source_name: Left Ovary

extract_protocol:
Tumors were dissociated using collagenase IV, Dnase I and hyaluronidase at 370C. Recovered single cells were run using the Drop-seq protocol; cells were lysed in droplet and mRNA was captured using barcode beads.
Libraries were prepared using Nextera XT DNA library preparation kit (FC-131-1096) following Illumina's instructions.

value: Left Ovary

tag: patient

tag: pathological stage

value: Low grade serous ovarian carcinoma (LGSOC)

tag: race

value: White

tag: neo-adjuvant

value: No


title: OvCa1131

description: Dropseq

source_name: Right Ovary

tag: tissue

value: Right Ovary

value: High grade serous ovarian carcinoma (HGSOC)

value: UNK


title: OvCa1134

description: Dropseq


title: OvCa1027

description: Dropseq

source_name: Omentum

value: Omentum


title: OvCa1028

description: Dropseq


title: OvCa1042

description: Dropseq


title: Lymph node sample 110, TCR

value: Lymph node

value: Lymphocytes


title: OvCa1175

description: Dropseq

value: Clear cell


title: OvCa3404

description: Dropseq


title: OvCa7019

description: Dropseq


title: OvCa2828

description: Dropseq

value: Malignant mixed Müllerian tumor (MMMT)

value: Asian

value: Yes


title: OvCa4137

description: Dropseq

value: Endometrioid and serous features


title: OvCa7055

description: Dropseq


title: OvCa6316

description: Dropseq

value: Endometrioid with serous features


title: OvCa2831

description: Dropseq


title: SRC141

status: Public on Dec 12 2023

first: Ajay

last: Subramanian

address: 450 Serra Mall

department: Radiation Oncology

institute: Stanford University School of Medicine

description: 10x Genomics

data_processing:
Sample demultiplexing, read alignment, and generation of feature-barcode matrices were performed using CellRanger v6.0.0 (10x Genomics).
Assembly: GRCh38.
Supplementary files format and content: Raw feature barcode matrix for downstream analysis.

source_name: Undifferentiated pleomorphic sarcoma

extract_protocol:
Fresh tumors were minced and enzymatically dissociated using the Human Tumor Dissociation Kit (Miltenyi Biotec) using a GentleMACS Octo Dissociator with heaters (Miltenyi Biotec) following the manufacturer’s instructions.
Libraries were constructed using the Chromium 3’ Gene Expression Solution v3.1 (10x Genomics) per the manufacturer’s instructions.

value: Undifferentiated pleomorphic sarcoma

value: Tumor


title: SRC164

description: 10x Genomics


title: DLS492, biol rep 2

status: Public on Dec 01 2023

city: Chapel Hill

first: Robert

middle: Houston

last: Dowen

state: NC

address: 321 Fordham Hall, CB7100

department: Cell Biology and Physiology

institute: University of North Carolina at Chapel Hill

description: Column_names: N2_r1, N2_r2, N2_r3, DLS316_r1, DLS316_r2, DLS316_r3, MT333_r1, MT333_r2, MT333_r3, DLS492_r1, DLS492_r2, DLS492_r3, DLS490_r1, DLS490_r2, DLS490_r3, DLS491_r1, DLS491_r2, DLS491_r3

data_processing:
The adapter-trimmed mRNA-Seq reads were mapped to the WS260 genome using the STAR aligner. The mapping was performed using a GTF obtained from Wormbase (c_elegans.PRJNA13758.WS260.canonical_geneset.gtf) with the parameter --outFilterIntronMotifs RemoveNoncanonical.
The gene-level read counts were calculated using the featureCounts algorithm of the subread package (Liao et al., Bioinformatics, 2014), using the following flags: -t exon -g gene_id -a c_elegans.PRJNA13758.WS260.canonical_geneset.gtf.
Differential expression was calculated relative to the N2 wild-type sample using the DESeq2 package using a 1% FDR cutoff (Love et al., 2014). Comparisons between double and single mutants were also performed.
Assembly: WS260
Supplementary files format and content: raw_gene_read_counts.txt: A tab-delimited text file that includes gene level unnormalized read counts for each sample in matrix format
Supplementary files format and content: DESeq2_norm_gene_counts.txt: A tab-delimited text file that includes gene level normalized read counts for each sample in matrix format
Supplementary files format and content: DESeq2_DEGs_sample1_v_sample2.txt: A tab-delimited text file that includes a list of differentially expressed genes, the log2 FC values, and the p values called by DESeq2 at a 1% FDR threshold for sample1 relative to sample2.

organism: Caenorhabditis elegans

source_name: Whole animals

growth_protocol: Wild-type and mutant C. elegans animals were synchronized at the L1 stage by egg prep and grown for ~72 hours at 20°C on 10cm NGM Agarose plates (5000 animals/plate) seeded with E. coli OP50 until they reached day 1 of adulthood.

extract_protocol:
Animals were harvested in M9 buffer, washed three times, and flash frozen in liquid Nitrogen. Total RNA was isolated using Trizol.
mRNA-Seq libraries were prepared using the Illumina TruSeq RNA Sample Preparation v2 kit

tag: genotype

value: Standard growth conditions at 20C on NGM plates containing E. coli OP50

tag: developmental stage

value: Day 1 adults

value: Whole animals

tag: sex

value: hermaphrodite


title: DLS492, biol rep 1

tag: treatment


title: DLS491, biol rep 2


title: DLS490, biol rep 2


title: DLS490, biol rep 1


title: DLS491, biol rep 3


title: DLS490, biol rep 3


title: DLS316, biol rep 1


title: MT333, biol rep 2


title: DLS492, biol rep 3


title: DLS316, biol rep 2


title: N2 wild-type, biol rep 2

value: wild-type


title: N2 wild-type, biol rep 1


title: MT333, biol rep 1


title: MT333, biol rep 3


title: Ovary, 9 months, 8

status: Public on Nov 27 2023

city: Oklahoma City

first: Michael

last: Stout

state: OK

address: 825 N.E. 13th Street

department: Aging and Metabolism

institute: Oklahoma Medical Research Foundation

data_processing:
Fastq files were generated and demultiplexed from raw base call (bcl) files using the cellranger mkfastq pipeline.
Alignment, filtering, barcode counting, and UMI counting were conducted using the cellranger count pipeline using the refdata-gex-mm10-2020-A reference transcriptome with default settings.
The resultant out files were loaded into R using the “load10X” function of the SoupX package.
The SoupX pipeline was then used to estimate and remove ambient RNA contamination before converting to Seurat objects
Samples were then merged to create a single Seurat object and filtered based on the number of features (>200) and percent mitochondrial transcripts (<25%). Genes that were expressed in less than three cells were removed from analysis. Genes that represent ribosomal contamination (Malat1, Gm42418, Gm26917, Ay036118) were causing technical background noises and were removed from the analysis to improve subclustering.
Variable features were identified in Seurat before scaling data and running PCA. The JackStraw method was used to determine the dimensionality of the dataset, and a UMAP analysis was generated in Seurat. Doublets were identified and removed using the DoubletFinder package with 5% doublets expected.
Other parameters (pN=0.25, pK=0.01) were generated using the DoubletFinder sweep statistics. Samples were co-projected on a UMAP which was used to determine that there were no batch effects and that further data integration was not necessary. Seurat was used to find differentially expressed genes by cluster and age and to generate plots presented in the figures (i.e., DimPlot, VlnPlot, DotPlot).
Assembly: refdata-gex-mm10-2020-A
Supplementary files format and content: Tab-separated values files and matrix files.
Supplementary files format and content: age.combined.RDS: Seurat object for all cell types from Figure 1.
Supplementary files format and content: Endothelial_Epithelial_Cells.rds: Seurat object for endothelial and epithelial cell subclusters.
Supplementary files format and content: Granulosa_Cells.rds: Seurat object for granulosa cell, oocytes, and luteal cells subcluster.
Supplementary files format and content: Immune_Cells.rds: Seurat Object for Immune Cell subclusters.
Supplementary files format and content: Stroma_Cells.rds: Seurat object for stroma and theca cell subclusters.

source_name: ovary

extract_protocol:
One ovary from each mouse was dissociated using a Multi Tissue Dissociation Kit 1 (cat#130110201, Miltenyi)
scRNA-Seq libraries were constructed with the Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3 (cat# 10000075, 10X Genomics)

value: ovary

value: 9 months old

value: female


title: N2 wild-type, biol rep 3


title: OvCa6370

description: Dropseq

source_name: Rectum

value: Rectum

value: White

value: No


title: Ovary, 9 months, 7


title: Ovary, 9 months, 6


title: DLS491, biol rep 1


title: DLS316, biol rep 3


title: Ovary, 9 months, 5


title: Ovary, 3 months, 2

value: 3 months old


title: Ovary, 3 months, 4


title: Ovary, 3 months, 3


title: Ovary, 3 months, 1


title: B16 xenograft, shHrs, replicate 5

status: Public on Oct 30 2023

city: PHILADELPHIA

first: Wei

last: Guo

state: PENNSYLVANIA

address: 433 S. University Avenue

institute: University of Pennsylvania

description:
B16 xenograft, shHrs, replicate 5
shHrs_5

data_processing:
Raw reads were processed by PennSCAP-T Next Generation Sequencing Pipeline (https://github.com/safisher/ngs). Basically, Illumina adapters were searched and trimmed from raw reads.
The processed reads were aligned to reference genome mm10 using STAR (v 2.4.0h2) (Dobin and Gingeras, 2015) with the parameters “--outFilterScoreMin 0 –outFilterScoreMinOverLread 0 –outFilterMatchNmin 30 --outFilterMatchNminOverLread 0.4 --outFilterMismatchNmax 100 --outFilterMismatchNoverLmax 0.3” and multiple alignments were filtered.
VERSE (v0.1.4) (Zhu et al. 2016) was used for count qualification with the parameters ‘-t "exon;mito;intron;intergenic" -z 3 –nonemptyModified’. Exonic counts were normalized by DESeq (Anders and Huber 2010).
Assembly: mm10
Supplementary files format and content: comma-delimited text file containing the gene-by-sample raw count matrix

source_name: tumor homograft model

growth_protocol: B16F10 cells were cultured in DMEM supplemented with 10% FBS and 1% penicillin/streptomycin. All cell lines were cultured in a 5% CO2 incubator at 37℃ and passaged every 2-3 days. 6 to 8-week-old female mice were used for all experiments. The wild type C57BL/6 mice were purchased from The Jackson Laboratory. Prior to all experiments, purchased mice were allowed one week to acclimate to housing conditions at The University of Pennsylvania Perelman School of Medicine Animal Facility. All experimental mice were housed in specific pathogen–free conditions and used in accordance with animal care guidelines from the University Laboratory Animal Resources (ULAR), University of Pennsylvania.

extract_protocol:
Total RNA was extracted from cultured control and HGS KD B16 cells, or the control and HGS KD B16 tumors harvested from tumor-bearing immunocompetent mice. The concentration of RNA was determined with Qubit® RNA Assay Kit in Qubit 2.0 Fluorometer (Life Technologies). RNA integrity was assessed with RNA Nano 6000 Assay Kit in the Bioanalyzer 2100 system (Agilent Technologies).
3 μg of RNA per sample were used to construct RNA-seq libraries. Sequencing libraries were generated using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (New England Biolabs, cat#E7530L) and sequenced on an Illumina Hiseq platform, and 125/150 bp paired‐end reads were generated (Novogene Bioinformatics Technology). Four biological repeats for B16 cells and five biological repeats for B16 tumors were performed for the RNA‐Seq experiment.

treatment_protocol: The shRNA oligos cloned in a pLKO.1-Puromycin+ (Puro) were obtained from the High-Throughput Screening Core at the University of Pennsylvania and Children’s Hospital of Philadelphia, and sequences for their respective target genes are listed in Key resources table. The shRNAs and scrambled shRNA (Addgene #1864) were packaged into lentiviral particles using HEK293T cells co-transfected with viral packaging plasmids. Lentiviral supernatants were harvested 48-72 hours after transfection by passing through a 0.45 μm filter. Collected lentivirus was used to infect cells in the presence of 8 μg/ml polybrene (Santa Cruz, cat#134220). Infected cells were selected and expanded with puromycin (Gold Biotechnology, cat#P-600-500) at 2 μg/ml or blasticidin (Sigma-Aldrich, cat#15205) at 5 μg/ml for 5 days before being used for subsequent experiments. Knockdown was verified by western blotting.

value: tumor homograft model

tag: cell line

tag: cell type

value: melanoma

value: shHrs


title: B16 xenograft, shCTL, replicate 4

description:
B16 xenograft, shCTL, replicate 4
shCTL_4

tag: strain

value: shCTL


title: B16 xenograft, shHrs, replicate 1

description:
B16 xenograft, shHrs, replicate 1
shHrs_1


title: B16 xenograft, shCTL, replicate 3

description:
B16 xenograft, shCTL, replicate 3
shCTL_3


title: B16 xenograft, shHrs, replicate 4

description:
B16 xenograft, shHrs, replicate 4
shHrs_4


title: B16 xenograft, shCTL, replicate 2

description:
B16 xenograft, shCTL, replicate 2
shCTL_2


title: B16 xenograft, shHrs, replicate 3

description:
B16 xenograft, shHrs, replicate 3
shHrs_3


title: B16 xenograft, shCTL, replicate 5

description:
B16 xenograft, shCTL, replicate 5
shCTL_5


title: B16 xenograft, shHrs, replicate 2

description:
B16 xenograft, shHrs, replicate 2
shHrs_2


title: B16 xenograft, shCTL, replicate 1

description:
B16 xenograft, shCTL, replicate 1
shCTL_1


description:
B16 cell line, batch 1, shCTL, replicate 2
R19051013

source_name: cell culture

value: cell culture


description:
B16 cell line, batch 1, shHrs, replicate 2
R19051014


description:
B16 cell line, batch 1, shCTL, replicate 1
R19051008


description:
B16 cell line, batch 1, shHrs, replicate 1
R19051009


description:
B16 cell line, batch 2, shCTL, replicate 2
R1908278


description:
B16 cell line, batch 2, shHrs, replicate 2
R1908276


description:
B16 cell line, batch 2, shHrs, replicate 1
R1908275


title: HumanNeuronCulturePositiveSingle, rep10

status: Public on Oct 19 2023

city: Philadelphia

first: Junhyong

last: Kim

state: PA

address: 433 S University Avenue

department: Biology

description: HumanNeuronCulturePositiveSingle

data_processing:
Base calls and demultiplexed using bcl2fastq v2.17. Reads were first preprocessed by a customized SCAP-T Next Generation Sequencing pipeline (https://github.com/safisher/ngs), then mapped back to the Gencode GRCh38 genome. Further, an additional QC procedure was applied to filter for high-quality reads with respect to the barcode/primer quality as well as the alignment quality. Basically, reads that qualify the A, B and C barcode/primer class are retained. Afterwards, reads that are less than 20bp (non-redundant length if paired) or have more than 10% mismatches are filtered out. Finally, reads that are mapped to low-quality genomic regions (defined by synthetic single-end 20bp reads that are mis-aligned to respective genomes) are removed. In addition, the ENCODE listed blacklist (https://sites.google.com/site/anshulkundaje/projects/blacklists) for human or mouse was used to mask the promiscuous regions. Finally, the starts (i.e. 5' end) of priming sites were called and output in the BED format, which were used for priming frequency estimation.
For priming start sites, we used R package ChIPseeker (v1.20.0) to annnote their genomic location with respect to promoter proximal as well as distal regions. To estimate the priming frequency, we used R package GenomicRanges v1.34.0. For priming frequency estimation, we used an in-house procedure to generate the aggreated coverage profiles at various genomic features, including TSS, gene body, intergenic, exon, intron, CDS. The genome annotation used for human was Ensembl v86 (via R package EnsDb.Hsapiens.v86), and for mouse was Ensembl v79 (via R package EnsDb.Mmusculus.v79).
Assembly: hg38
Supplementary files format and content: BED files containing the 5' location of CHEX-seq probe priming
Library strategy: CHEX-seq

source_name: brain

growth_protocol: Human brain tissue was collected at the Hospital of the University of Pennsylvania (IRB#816223) using standard operating procedures for enrollment and consent of patients. Briefly, an en bloc sample of brain (typically 5x5x5 mm) was obtained from cortex that was resected as part of neurosurgical procedures for the treatment of epilepsy or brain tumors. From them astrocytes and neurons were cultured and harvested as the HumanAstroCulture and HumanNeuronCulture samples.

extract_protocol:
After fixation and permeabilization, the cells and brain slices were incubated with CHEX-seq probe (170 nM) in TES buffer (10 mM Tris, 1 mM EDTA, 150 mM NaCl) for 1 hr at room temperature. The samples were then washed with 1x PBS (w/o Ca++, Mg++) 3 times for 3 min. After CHEX-seq probe annealing and washing, the samples were transferred to the imaging chamber with 1x PBS (w/o Ca++, Mg++). All images and photoactivations were performed using a Carl Zeiss 710 Meta confocal microscope (20x water-immersion objectives, NA 1.0). CHEX-seq probe annealing was confirmed by exciting at 633 nm and emission was detected at 640-747 nm. The photoactivation was performed using the 405 nm (UV) laser at 60% power and 6.30 μs per pixel. After photoactivation in each individual cell’s nucleus, a master mix containing DNA polymerase I and 1st strand DNA synthesis buffer was added to the cells and incubated for 1 h at room temperature. Subsequently, the single cells containing synthesized complementary DNA were harvested using a glass micropipette under using a Zeiss 710 confocal microscope (Carl Zeiss) for visualization.
(A) 1st strand DNA synthesis and poly G tailing at 3’ end: After harvesting single cells, the in situ synthesized cDNA was removed by adding fresh prepared 0.1 N NaOH and incubating the sample for 5 min at RT followed by neutralization with 1 M Tris (pH 7.5). After ethanol precipitation, the 1st strand DNA was resuspended in nuclease free water. Subsequently, poly(G) was added to the 3’ end using terminal deoxynucleotidyl transferase (TdT) (Invitrogen). (B) 2nd strand DNA synthesis and round 1 linear RNA amplification: 2nd strand DNA was synthesized using DNA polymerase I for 2 h at 16 °C after priming with custom App-RC-polyC primer (Supplemental Data, Table 1). RNA was amplified using linear in vitro transcription from T7 RNA polymerase promoter incorporated into the double-stranded DNA with Ambion MEGAscript T7 In Vitro Transcription (IVT) Kit. (C) Round 2 1st and 2nd strand DNA synthesis and PCR amplification: After cleanup IVT reaction, 1st strand DNA was reverse transcribed from aRNA using Superscript III using a custom App-RC primer (Supplemental Data, Table 1) 2nd strand DNA was synthesized using DNA Polymerase 1 with a custom 18bpPBC1 primer (Supplemental Data, Table 1). Subsequently, the double-stranded blunt ended DNA was amplified using custom primers 18bpPBC1 / App-RC (Supplemental Data, Table 1) following PCR condition: 98 °C for 30 sec; thermocycling at 98 °C for 10 sec, 50 °C for 30 sec, 72 °C for 30 sec for 27 cycles; extension at 72 °C for 2 mins, and was then used for library construction. Samples for the control experiments were processed with the same procedure except no CHEX-seq probe was applied, and 2nd round 2nd strand DNA PCR amplification was performed with custom primers 18bpPBC14 / App-RC. Illumina TruSeq Nano DNA Library Preparation Kit was used with modifications. All of the second round PCR amplified double-stranded DNA was used as input. After converting DNA fragment into blunt ends with End Repair Mix, base “A” was added; sequence adapters were ligated. DNA inserts were amplified with PCR.

treatment_protocol: The cultured cells were transferred to a 50 ml tube and 16% paraformaldehyde (final 1%) was added for 10 mins at room temperature to fix the cells. After fixation, 1 M glycine (final 200 mM) with RPMI 1640 medium was used to quench for 10 mins followed by centrifugation at 300 x g for 5 mins. The supernatant was discarded and - 3 mL of PBS were added to the pellet and then mixed by gently pipetting up and down 10-15 times using a fire-polished glass-pipette, to prevent cell clumping, and centrifuged at 300 rpm for 5 mins. The 100 μl cell pellet was attached to 18 mm gridded coverslips by incubating them for 2 hr. at room temperature. The samples were treated with PBS (w/o Ca++, Mg++) containing 0.01% Triton X-100 for 10 mins and then washed with PBS (w/o Ca++, Mg++) 3 times for 3 mins. To prepare human neuronal cell cultures, adult human brain tissue was placed in the papain (20 U, Worthington Biochemical) solution to dissociate at 37 °C for 30 to 40 mins and followed by ovomucoid (a papain inhibitor, 10 mg/ml, Worthington Biochemical) to stop the enzymatic dissociation. The tissue was triturated with a fire-polished glass Pasteur pipette. The cloudy cell suspension was carefully transferred to a new tube and centrifuged at 300 x g for 5 mins at room temperature. The cells were counted in an Autocounter (Invitrogen). Cells were plated on poly-L-lysine-coated (0.1 mg/ml, Sigma-Aldrich) 12-mm coverslips at a density of 3 × 104 cells/coverslip. Cultures were incubated at 37 °C, 95% humidity, and 5% CO2 in neuronal basal medium (Neurobasal A, Gibco), serum-free supplement (B-27, Gibco) and 1% penicillin/streptomycin (Thermo-Fisher Scientific). Dispersed mouse neuron/astrocyte cultures were prepared following published protocols. Dispersed cells were fixed using 4% paraformaldehyde for 10 min at room temperature. This was followed by three washes with 1x PBS. The cells were permeabolized with 0.1% Triton-X100 for 10 min at room temperature followed by three washes with 1x PBS.

value: brain

value: neuron

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value: Single

tag: biological group

value: HumanNeuronCulture

tag: treatment group

value: PositiveSingle


title: HumanNeuronCulturePositiveSingle, rep12

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title: HumanNeuronCulturePositiveSingle, rep11

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title: HumanNeuronCulturePositiveSingle, rep7

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title: HumanNeuronCulturePositiveSingle, rep6

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title: HumanNeuronCulturePositiveSingle, rep4

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title: HumanNeuronCulturePositiveSingle, rep2

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title: HumanNeuronCulturePositiveSingle, rep1

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title: HumanAstroCulturePositiveSingle, rep2

description: HumanAstroCulturePositiveSingle

tag: tissue

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value: astrocyte

tag: genotype

value: HumanAstroCulture


title: HumanAstroCulturePositiveSingle, rep1

description: HumanAstroCulturePositiveSingle

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title: HumanAstroCulturePositiveSingle, rep4

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title: HumanAstroCulturePositiveSingle, rep5

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description:
B16 cell line, batch 2, shCTL, replicate 1
R1908277

tag: strain

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title: HumanAstroCulturePositiveBulk, rep1

description: HumanAstroCulturePositiveBulk

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value: Bulk

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value: PositiveBulk


title: HumanAstroCulturePositiveBulk, rep2

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title: K562TPAnonePositiveSingle, rep1

data_processing:
Base calls and demultiplexed using bcl2fastq v2.17. Reads were first preprocessed by a customized SCAP-T Next Generation Sequencing pipeline (https://github.com/safisher/ngs), then mapped back to the Gencode GRCh38 (human) or UCSC mm10 (mouse) genome. Further, an additional QC procedure was applied to filter for high-quality reads with respect to the barcode/primer quality as well as the alignment quality. Basically, reads that qualify the A, B and C barcode/primer class are retained. Afterwards, reads that are less than 20bp (non-redundant length if paired) or have more than 10% mismatches are filtered out. Finally, reads that are mapped to low-quality genomic regions (defined by synthetic single-end 20bp reads that are mis-aligned to respective genomes) are removed. In addition, the ENCODE listed blacklist (https://sites.google.com/site/anshulkundaje/projects/blacklists) for human or mouse was used to mask the promiscuous regions. Finally, the starts (i.e. 5' end) of priming sites were called and output in the BED format, which were used for priming frequency estimation.
For priming start sites, we used R package ChIPseeker (v1.20.0) to annnote their genomic location with respect to promoter proximal as well as distal regions. To estimate the priming frequency, we used R package GenomicRanges v1.34.0. For priming frequency estimation, we used an in-house procedure to generate the aggreated coverage profiles at various genomic features, including TSS, gene body, intergenic, exon, intron, CDS. The genome annotation used for human was Ensembl v86 (via R package EnsDb.Hsapiens.v86), and for mouse was Ensembl v79 (via R package EnsDb.Mmusculus.v79).
Assembly: hg38, mm10
Supplementary files format and content: BED files containing the 5' location of CHEX-seq probe priming
Library strategy: CHEX-seq

source_name: bone marrow

growth_protocol: K562 cells were obtained from ATCC and cultured in RPMI 1640 medium (Invitrogen) with 10% FBS and penicillin-streptomycin in a T75 flask at 37 °C in 5% CO2 for 2~3 days. HumanInterneuronCulture samples were derived from human induced pluripotent stem cells (iPSCs), where Stewart-4wk-human stem cells from the Children's Hospital of Philadelphia (CHOP) were plated on rat cortical neuronal feeders-1 and selected by interneuron promoter Lhx6-driven GFP expression. For mouse samples, a 3-month old male mouse was anaesthetized with halothane, euthanized by thoracotomy, then subjected to cardiac perfusion with 5 ml PBS followed by 20 ml PBS/4% paraformaldehyde. The brain was removed and post fixed at 4 °C for 16 hr., then rinsed in PBS and sectioned in the coronal plane at 100 μm on a vibratome (Leica VT-1000s). Sections including the hippocampus were then subjected to immunofluorescence labeling with chicken anti-MAP2 antisera (1:1000; Ab 5392; Abcam) followed by Alexa 488 conjugated goat anti-chicken secondary antibody (1:400; ab150169; Abcam).

value: bone marrow

value: blood

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title: K562TPA2hrPositiveSingle, rep12

tag: tissue

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title: K562TPA2hrPositiveSingle, rep13

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title: K562TPA2hrPositiveSingle, rep7

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tag: genotype

tag: probe id

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title: K562TPA2hrPositiveSingle, rep10

tag: primer pc

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title: K562TPAnonePositiveSingle, rep2

tag: cell count

tag: harvest method

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title: K562TPAnonePositiveSingle, rep3

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title: K562TPA2hrPositiveSingle, rep8

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title: K562TPA2hrPositiveSingle, rep3

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title: K562TPA2hrPositiveSingle, rep9

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title: K562TPA2hrPositiveSingle, rep6

tag: cell count

tag: harvest method

tag: has tpa

tag: tpa dose


title: K562TPA2hrPositiveSingle, rep1

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tag: cell line

tag: tpa time

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title: K562TPA2hrPositiveSingle, rep4

tag: is negative_control

tag: composition

tag: biological group

tag: treatment group


title: HumanAstroCulturePositiveSingle, rep3

description: HumanAstroCulturePositiveSingle

tag: cell type

tag: genotype

tag: probe id

tag: primer 2p


title: K562TPA2hrPositiveSingle, rep5

tag: primer pc

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title: K562TPA2hrPositiveSingle, rep2

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tag: harvest method

tag: has tpa

tag: tpa dose


title: K562TPA24hrPositiveSingle, rep4

tag: tissue

tag: cell line

tag: tpa time

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title: K562TPA24hrPositiveSingle, rep5

tag: is negative_control

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title: HumanNeuronCulturePositiveSingle, rep5

description: HumanNeuronCulturePositiveSingle

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title: K562TPA24hrPositiveSingle, rep3

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title: K562TPA24hrPositiveSingle, rep1

tag: cell count

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title: K562TPA2hrPositiveSingle, rep11

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title: K562TPA1hrPositiveSingle, rep3

tag: is negative_control

tag: composition

tag: biological group

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title: K562TPA1hrPositiveSingle, rep2

tag: cell type

tag: genotype

tag: probe id

tag: primer 2p


title: K562TPA1hrPositiveSingle, rep5

tag: primer pc

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title: K562TPA1hrPositiveSingle, rep4

tag: cell count

tag: harvest method

tag: has tpa

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title: K562TPA15minPositiveSingle, rep5

tag: tissue

tag: cell line

tag: tpa time

tag: has mung_bean


title: K562TPA1hrPositiveSingle, rep1

tag: is negative_control

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title: K562TPA24hrPositiveSingle, rep2

tag: cell type

tag: genotype

tag: probe id

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title: K562TPA15minPositiveSingle, rep4

tag: primer pc

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title: K562TPA15minPositiveSingle, rep3

tag: cell count

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title: K562TPA15minPositiveSingle, rep2

tag: tissue

tag: cell line

tag: tpa time

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title: K562PositiveSingle, rep74

tag: is negative_control

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title: K562PositiveSingle, rep71

tag: cell type

tag: genotype

tag: probe id

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title: K562PositiveSingle, rep73

tag: primer pc

tag: has probe

tag: has laser405

tag: has laser633


title: K562TPA15minPositiveSingle, rep1

tag: cell count

tag: harvest method

tag: has tpa

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title: K562PositiveSingle, rep68

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title: K562PositiveSingle, rep67

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title: K562PositiveSingle, rep64

tag: primer pc

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title: K562PositiveSingle, rep63

tag: cell count

tag: harvest method

tag: has tpa

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title: K562PositiveSingle, rep66

tag: tissue

tag: cell line

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title: K562PositiveSingle, rep61

tag: is negative_control

tag: composition

tag: biological group

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title: K562PositiveSingle, rep62

tag: cell type

tag: genotype

tag: probe id

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title: K562PositiveSingle, rep60

tag: primer pc

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title: K562PositiveSingle, rep59

tag: cell count

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tag: has tpa

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title: K562PositiveSingle, rep58

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title: K562PositiveSingle, rep57

tag: is negative_control

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title: K562PositiveSingle, rep55

tag: cell type

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title: K562PositiveSingle, rep75

tag: primer pc

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title: K562PositiveSingle, rep53

tag: cell count

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title: K562PositiveSingle, rep72

tag: tissue

tag: cell line

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title: K562PositiveSingle, rep70

tag: is negative_control

tag: composition

tag: biological group

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title: K562PositiveSingle, rep51

tag: cell type

tag: genotype

tag: probe id

tag: primer 2p


title: K562PositiveSingle, rep48

tag: primer pc

tag: has probe

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title: K562PositiveSingle, rep49

tag: cell count

tag: harvest method

tag: has tpa

tag: tpa dose


title: K562PositiveSingle, rep47

tag: tissue

tag: cell line

tag: tpa time

tag: has mung_bean


title: K562PositiveSingle, rep46

tag: is negative_control

tag: composition

tag: biological group

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title: K562PositiveSingle, rep65

tag: cell type

tag: genotype

tag: probe id

tag: primer 2p


title: K562PositiveSingle, rep42

tag: primer pc

tag: has probe

tag: has laser405

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title: K562PositiveSingle, rep45

tag: cell count

tag: harvest method

tag: has tpa

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title: K562PositiveSingle, rep40

tag: tissue

tag: cell line

tag: tpa time

tag: has mung_bean


title: K562PositiveSingle, rep44

tag: is negative_control

tag: composition

tag: biological group

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title: K562PositiveSingle, rep41

tag: cell type

tag: genotype

tag: probe id

tag: primer 2p


title: K562PositiveSingle, rep39

tag: primer pc

tag: has probe

tag: has laser405

tag: has laser633


title: K562PositiveSingle, rep37

tag: cell count

tag: harvest method

tag: has tpa

tag: tpa dose